Just a suggestion, but I was running into package-related segfaults on Rdevel last week. I believe Martin Maechler committed a fix for some of these issues on Sunday. Might be worth checking if these errors are visible using the latest Rdevel or just the RC.
Keith > On Apr 17, 2018, at 11:04 AM, Martin Morgan <martin.mor...@roswellpark.org> > wrote: > > The stack trace looks like it's an Rcpp problem (topic of this mailing list) > maybe with a finalizer running at an unexpected time for what it wants to > accomplish. R-3.5 is in release candidate so highly relevant to the user > community even if not R-devel. If this list can help rule out Rcpp or help > point to the offending user of Rcpp or otherwise identify the problem that > would be great... > > Martin > >>> On 04/17/2018 10:55 AM, Jeff Newmiller wrote: >>> R v3.5 is still off-topic on this mailing list. Try R-devel. >>> On April 17, 2018 6:38:40 AM PDT, "Shepherd, Lori" >>> <lori.sheph...@roswellpark.org> wrote: >>> I starting running into an issue trying to install certain packages >>> where I encounter a segfault. I can also install packages but then >>> upon quitting R I get a segfault. >>> >>> >>> lori@lori-HP-ZBook-15-G2:~$ R CMD config CC >>> gcc >>> lori@lori-HP-ZBook-15-G2:~$ R CMD config CXX >>> g++ >>> >>> lori@lori-HP-ZBook-15-G2:~$ g++ --version >>> g++ (Ubuntu 5.4.1-2ubuntu1~14.04) 5.4.1 20160904 >>> Copyright (C) 2015 Free Software Foundation, Inc. >>> This is free software; see the source for copying conditions. There is >>> NO >>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >>> PURPOSE. >>> >>> lori@lori-HP-ZBook-15-G2:~$ gcc --version >>> gcc (Ubuntu 5.4.1-2ubuntu1~14.04) 5.4.1 20160904 >>> Copyright (C) 2015 Free Software Foundation, Inc. >>> This is free software; see the source for copying conditions. There is >>> NO >>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >>> PURPOSE. >>> >>> >>> >>> >>> As an example. I was trying to install the package erma. >>> http://bioconductor.org/packages/release/bioc/html/erma.html >>> >>> According to the description it seems like shiny and ggplot2 are likely >>> the only dependencies that would load Rcpp >>>  >>> >>> lori@lori-HP-ZBook-15-G2:~/b/Rpacks$ R CMD INSTALL --no-test-load erma >>> Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help >>> * installing to library >>> '/home/lori/R/x86_64-pc-linux-gnu-library/3.5-BioC-3.7' >>> * installing *source* package 'erma' ... >>> ** R >>> ** data >>> ** inst >>> ** byte-compile and prepare package for lazy loading >>> ** help >>> *** installing help indices >>> ** building package indices >>> ** installing vignettes >>> * DONE (erma) >>> >>> *** caught segfault *** >>> address (nil), cause 'memory not mapped' >>> An irrecoverable exception occurred. R is aborting now ... >>> Segmentation fault >>> >>> >>> >>> The package installed but then when I do a library("erma") and quit R >>> the segfault message also appears. When I tried debugging with >>> valgrind, it provided the following output: >>> >>> >>> >>> lori@lori-HP-ZBook-15-G2:/tmp/Rcpp$ cat erma.valgrind >>> ==22933== Memcheck, a memory error detector >>> ==22933== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et >>> al. >>> ==22933== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright >>> info >>> ==22933== Command: /home/lori/bin/R-3-5-branch/bin/exec/R -e >>> library(erma) >>> ==22933== >>> >>> R version 3.5.0 beta (2018-04-09 r74559) -- "Joy in Playing" >>> Copyright (C) 2018 The R Foundation for Statistical Computing >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>> You are welcome to redistribute it under certain conditions. >>> Type 'license()' or 'licence()' for distribution details. >>> >>> Natural language support but running in an English locale >>> >>> R is a collaborative project with many contributors. >>> Type 'contributors()' for more information and >>> 'citation()' on how to cite R or R packages in publications. >>> >>> Type 'demo()' for some demos, 'help()' for on-line help, or >>> 'help.start()' for an HTML browser interface to help. >>> Type 'q()' to quit R. >>> >>> Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help >>>> library(erma) >>> Loading required package: Homo.sapiens >>> Loading required package: AnnotationDbi >>> Loading required package: stats4 >>> Loading required package: BiocGenerics >>> Loading required package: parallel >>> >>> Attaching package: 'BiocGenerics' >>> >>> The following objects are masked from 'package:parallel': >>> >>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >>> clusterExport, clusterMap, parApply, parCapply, parLapply, >>> parLapplyLB, parRapply, parSapply, parSapplyLB >>> >>> The following objects are masked from 'package:stats': >>> >>> IQR, mad, sd, var, xtabs >>> >>> The following objects are masked from 'package:base': >>> >>> anyDuplicated, append, as.data.frame, basename, cbind, colMeans, >>> colnames, colSums, dirname, do.call, duplicated, eval, evalq, >>> Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, >>> lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, >>> pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, >>> rowSums, sapply, setdiff, sort, table, tapply, union, unique, >>> unsplit, which, which.max, which.min >>> >>> Loading required package: Biobase >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material; view with >>> 'browseVignettes()'. To cite Bioconductor, see >>> 'citation("Biobase")', and for packages 'citation("pkgname")'. >>> >>> Loading required package: IRanges >>> Loading required package: S4Vectors >>> >>> Attaching package: 'S4Vectors' >>> >>> The following object is masked from 'package:base': >>> >>> expand.grid >>> >>> Loading required package: OrganismDbi >>> Loading required package: GenomicFeatures >>> Loading required package: GenomeInfoDb >>> Loading required package: GenomicRanges >>> Loading required package: GO.db >>> >>> Loading required package: org.Hs.eg.db >>> >>> Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene >>> Loading required package: GenomicFiles >>> Loading required package: SummarizedExperiment >>> Loading required package: DelayedArray >>> Loading required package: matrixStats >>> >>> Attaching package: 'matrixStats' >>> >>> The following objects are masked from 'package:Biobase': >>> >>> anyMissing, rowMedians >>> >>> Loading required package: BiocParallel >>> >>> Attaching package: 'DelayedArray' >>> >>> The following objects are masked from 'package:matrixStats': >>> >>> colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges >>> >>> The following objects are masked from 'package:base': >>> >>> aperm, apply >>> >>> Loading required package: Rsamtools >>> Loading required package: Biostrings >>> Loading required package: XVector >>> >>> Attaching package: 'Biostrings' >>> >>> The following object is masked from 'package:DelayedArray': >>> >>> type >>> >>> The following object is masked from 'package:base': >>> >>> strsplit >>> >>> Loading required package: rtracklayer >>> ==22933== Invalid read of size 4 >>> ==22933== at 0x8CC0443: std::locale::~locale() (in >>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19) >>> ==22933== by 0x1DDE0572: ~basic_streambuf (streambuf:198) >>> ==22933== by 0x1DDE0572: ~Rstreambuf (Rstreambuf.h:31) >>> ==22933== by 0x1DDE0572: Rcpp::Rostream<false>::~Rostream() >>> (Rstreambuf.h:44) >>> ==22933== by 0x6E2E1A8: __run_exit_handlers (exit.c:82) >>> ==22933== by 0x6E2E1F4: exit (exit.c:104) >>> ==22933== by 0x5EA95F: Rstd_CleanUp (sys-std.c:1213) >>> ==22933== by 0x511082: end_Rmainloop (main.c:1072) >>> ==22933== by 0x511082: run_Rmainloop (main.c:1083) >>> ==22933== by 0x41B607: main (Rmain.c:29) >>> ==22933== Address 0x0 is not stack'd, malloc'd or (recently) free'd >>> ==22933== >>> >>> *** caught segfault *** >>> address (nil), cause 'memory not mapped' >>> An irrecoverable exception occurred. R is aborting now ... >>> ==22933== >>> ==22933== HEAP SUMMARY: >>> ==22933== in use at exit: 577,597,056 bytes in 135,393 blocks >>> ==22933== total heap usage: 661,662 allocs, 526,269 frees, >>> 1,380,607,407 bytes allocated >>> ==22933== >>> ==22933== LEAK SUMMARY: >>> ==22933== definitely lost: 0 bytes in 0 blocks >>> ==22933== indirectly lost: 0 bytes in 0 blocks >>> ==22933== possibly lost: 1,591,450 bytes in 2,158 blocks >>> ==22933== still reachable: 576,005,606 bytes in 133,235 blocks >>> ==22933== suppressed: 0 bytes in 0 blocks >>> ==22933== Rerun with --leak-check=full to see details of leaked memory >>> ==22933== >>> ==22933== For counts of detected and suppressed errors, rerun with: -v >>> ==22933== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from >>> 0) >>> >>> >>> >>> >>> Any advice on how to remedy this situation is greatly appreciated. >>> >>> >>> >>> Lori Shepherd >>> >>> Bioconductor Core Team >>> >>> Roswell Park Cancer Institute >>> >>> Department of Biostatistics & Bioinformatics >>> >>> Elm & Carlton Streets >>> >>> Buffalo, New York 14263 >>> >>> >>> This email message may contain legally privileged and/or confidential >>> information. If you are not the intended recipient(s), or the employee >>> or agent responsible for the delivery of this message to the intended >>> recipient(s), you are hereby notified that any disclosure, copying, >>> distribution, or use of this email message is prohibited. If you have >>> received this message in error, please notify the sender immediately by >>> e-mail and delete this email message from your computer. Thank you. > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. 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